This dataset comprises whole-genome sequencing data for Helicobacter pylori (H. pylori), collected from publicly available databases, including NCBI (https://www.ncbi.nlm.nih.gov/) and BV-BRC(https://www.bv-brc.org/). The data was originally generated and submitted to these databases as part of various studies focused on understandingantibiotic resistance of H. pylori.For further information on the studies that contributed to this dataset, please refer to the original research publications("Early genetic diagnosis of clarithromycin resistance in Helicobacter pylori", "Helicobacter pylori Infections in the Bronx, New York: Surveying Antibiotic Susceptibility and Strain Lineage by Whole-Genome Sequencing", "Helicobacter pylori Antimicrobial Resistance and Gene Variants in High- and Low-Gastric-Cancer-Risk Populations", "A Survey of Helicobacter pylori Antibiotic-Resistant Genotypes and Strain Lineages by Whole-Genome Sequencing in China", "Multiple Genome Sequences of Helicobacter pylori Strains of Diverse Disease and Antibiotic Resistance Backgrounds from Malaysia", "Long-Read- and Short-Read-Based Whole-Genome SequencingReveals the Antibiotic Resistance Pattern of Helicobacter pylori", "Antimicrobial resistance patterns and genetic elements associated with the antibiotic resistance of Helicobacter pylori strains from Shanghai") and the associated GenBank accessions, which can be found in the file GenBank Accessions.txt. This file provides a detailed list of the accession numbers, allowing you to access the specific genetic sequences and related data used in this study.

This dataset contains low-coverage whole genome sequencing (lcWGS) data from multiple subspecies of white-crowned sparrows (Zonotrichia leucophrys) sampled across Alberta and British Columbia (Canada), and Colorado and Oregon (USA), between 2017 and 2021. The samples represent three focal subspecies (Z. l. gambelii, Z. l. oriantha, and Z. l. pugetensis) collected during the breeding season from riparian deciduous habitats to minimize environmental effects on genetic variation.

Genomic DNA was extracted from blood or feather samples using a modified salt extraction method, and shotgun sequencing libraries were prepared without PCR amplification, incorporating 8 bp unique barcodes per sample. Sequencing was performed at Genome Quebec using Illumina NovaSeq 6000 S4 PE 150 chemistry. Each sample was sequenced at a depth of ~6.2x to 8.9x coverage.

The data processing pipeline includes read alignment to the zebra finch (Taeniopygia guttata) reference genome using BWA, duplicate removal with Picard, indel realignment and overlap clipping, genotype likelihood estimation with SAMtools and BCFtools, and SNP calling with quality and frequency filters. ANGSD was used to infer major/minor alleles, allele frequencies, and to generate population-level variant data for downstream analysis of genetic structure and divergence. This dataset supports investigations into mitonuclear coevolution, population structure, and recent divergence patterns in white-crowned sparrows.

data_Genbank_june2017Each file contains the metadata of genomes available in GenBank for a given taxonomic group up to June 2017 (https://www.ncbi.nlm.nih.gov/genome/browse/#). Four levels of assembly were considered: contigs, scaffolds, chromosomes, and complete genome (https://www.ncbi.nlm.nih.gov/assembly/help/#definition).

The complete genome sequence data of S. aureus SJTUF_J27 isolated from seaweed in China is reported here. The size of the genome is 2.8 Mbp with 32.9% G+C content, consisting of 2614 coding sequences and 77 RNAs. A number of virulence factors, including antimicrobial resistance genes (fluoroquinolone, beta-lactams, fosfomycin, mupirocin, trimethoprim, and aminocoumarin) and the egc enterotoxin cluster, were found in the genome. In addition, the genes encoding metal-binding proteins and associated heavy metal resistance were identified. Phylogenetic data analysis, based upon genome-wide single nucleotide polymorphisms (SNPs), and comparative genomic evaluation with BLAST Ring Image Generator (BRIG) were performed for SJTUF_J27 and four S. aureus strains isolated from food. The completed genome data was deposited in NCBI's GenBank under the accession number CP019117, https://www.ncbi.nlm.nih.gov/nuccore/CP019117. Resources in this dataset: Resource Title: NCBI GenBank Accession CP019117.1: Staphylococcus aureus strain SJTUF_J27 chromosome, complete genome. File Name: Web Page, url: https://www.ncbi.nlm.nih.gov/nuccore/CP019117 With an average of 331-fold sequencing coverage, a genome size of 2,804,759 bp constituting 32.9% of G+C content was generated. RAST annotation of the genome revealed a total of 399 subsystems, 2614 coding sequences (80 of them related to virulence, disease and defense), and 77 RNAs. PathogenFinder showed the probability of this strain being a human pathogen was 98%. Bacteria and source DNA available from Xianming Shi, 800 Dongchuan Road, Shanghai, China, 200240. Annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (released 2013).

The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis. This dataset is a filtered search result in the GDC Data Portal for TCGA Project, Adenocarcinoma, Whole Genome Sequencing Reads. It consists of 196 BAM files and 99 cases.

Whole-genome sequencing of caucasian male. Replicate 3

Whole-genome sequencing data statistics.

This dataset comes from shallow whole genome sequencing data of STIC project

Supercentenarians (110 years or older) are the world’s oldest people. Seventy four are alive worldwide, with twenty two in the United States. We performed whole-genome sequencing on 17 supercentenarians to explore the genetic basis underlying extreme human longevity. We found no significant evidence of enrichment for a single rare protein-altering variant or for a gene harboring different rare protein altering variants in supercentenarian compared to control genomes. We followed up on the gene most enriched for rare protein-altering variants in our cohort of supercentenarians, TSHZ3, by sequencing it in a second cohort of 99 long-lived individuals but did not find a significant enrichment. The genome of one supercentenarian had a pathogenic mutation in DSC2, known to predispose to arrhythmogenic right ventricular cardiomyopathy, which is recommended to be reported to this individual as an incidental finding according to a recent position statement by the American College of Medical Genetics and Genomics. Even with this pathogenic mutation, the proband lived to over 110 years. The entire list of rare protein-altering variants and DNA sequence of all 17 supercentenarian genomes is available as a resource to assist the discovery of the genetic basis of extreme longevity in future studies.

The data release details the samples, methods, and raw data used to generate high-quality genome assemblies for greater sage-grouse (Centrocercus urophasianus), white-tailed ptarmigan (Lagopus leucura), and trumpeter swan (Cygnus buccinator). The raw data have been deposited in the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI), the authoritative repository for public biological sequence data, and are not included in this data release. Instead, the accessions that link to those data via the NCBI portal (www.ncbi.nlm.nih.gov) are provided herein. The release consists of a single file, sample.metadata.txt, which maps NCBI accessions to the samples sequenced and the different types of sequencing performed to generate the assemblies and annotate their gene features.

Manually curated database of all conditions with known genetic causes, focusing on medically significant genetic data with available interventions. Includes gene symbol, conditions, allelic conditions, inheritance, age in which interventions are indicated, clinical categorization, and general description of interventions/rationale. Contents are intended to describe types of interventions that might be considered. Includes only single gene alterations and does not include genetic associations or susceptibility factors related to more complex diseases.

The dataset contains whole genome sequencing data of 58 high-grade serous carcinoma (HGSC) patients sequenced with Novoseq 6000. The 144 samples are either fresh frozen tumour samples or blood samples. The files provided are paired fastq files.

The global Genomic Data Analysis Service market is booming, projected to reach $4192.3 million in 2025, with a significant CAGR driving growth. Explore market trends, key players (Illumina, QIAGEN, BGI Genomics), and regional insights in this comprehensive analysis. Discover opportunities in whole genome & exome sequencing.

This dataset represent long read sequencing of single human T cells isolated from a human donor. The data set include Illumina whole genome sequencing of 16 single T cells and PacBio HiFi whole genome sequenicng of 5 single T cells

kraken2 database of common marine animal hosts in marine metagenomic dataset. Used in Nephele pipelines for decontamination of metagenomic datasets from common marine animal host reads (database inclusive of human genome).

Content of assemblies:

Whole-genome sequencing (WGS) data.

4-thiouracil suppressor bacterial whole genome sequencing files

GeoMx Whole Genome Sequencing processed datasets from Goyal et al.. All raw data from the Whole Genome Sequencing used in this manuscript can be found at BioProject Accession PRJNA972638.

This dataset contains concordance metrics between high and low-coverage VCF files of the IBS001 genome, belonging to an IBS (Iberian Populations in Spain) individual. This genome was sequenced at 40X coverage in both Illumina and MGI sequencing platforms, and then respectively downsampled to 1x coverage with samtools. Genotype likelihood calculations and calling was performed using bcftools, and imputation of the low-coverage genotypes was performed using GLIMPSE1.See related materials at: https://doi.org/10.25452/figshare.plus.c.6347534

Whole Genome Shotgun (WGS) projects are genome assemblies of incomplete genomes or incomplete chromosomes of prokaryotes or eukaryotes that are generally being sequenced by a whole genome shotgun strategy. WGS projects may be annotated, but annotation is not required. NCBI has a Prokaryotic Genomes Annotation Pipeline that may be requested at the time the genome files are submitted to GenBank. This pipeline generates a submission-ready annotated file that is posted back to the submitter for review and which the submitter could edit prior to data release. The public WGS projects are at the list of WGS projects. https://www.ncbi.nlm.nih.gov/Traces/wgs/